Read counts summary

1 Requirements

• if not all dependencies are satisfied by R environment, try to install additional libraries dplyr, ggplot2, tidyr, Hmisc
• loading libraries

[1] "Required package(s) dplyr, ggplot2, tidyr, Hmisc are already installed."

• loading libraries

[1] "Required package(s) dplyr, ggplot2, tidyr, Hmisc are loaded."

2 Sample overview

2.1 Data import

• Checking if result file(s) are available:

• Importing result table(s):

[1] "Import of counts table complete."

2.2 Sample table

• overview of samples

3 Quality control

3.1 Total number of mapped reads per sample

3.2 Number of individual barcodes per sample

3.3 Number of missing barcodes per sample

3.4 Number of barcodes per gene, per sample

`summarise()` has grouped output by 'sample'. You can override using the
`.groups` argument.

3.5 Read count distribution, per sample (capped at 1000 barcodes)

3.6 Number of reads per barcode, per sample

3.7 Top 10 most abundant barcodes, per sample

3.8 Cumulative read count distribution and population equality

3.9 Sample and replicate correlation coefficent (R)

3.10 Sample and replicate similarity with PCA

4 Report info

The template for this report is located in ./nf-core-crispriscreen/bin/counts_summary.Rmd.

Date: 2022-04-28

Author: Michael Jahn, PhD

Affilations:

• Science For Life Laboratory (KTH), Stockholm, Sweden
• Max-Planck-Unit for the Science of Pathogens, Berlin, Germany

5 Session Info

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=sv_SE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=sv_SE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=sv_SE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=sv_SE.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Stockholm
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Hmisc_5.1-1   tidyr_1.3.0   ggplot2_3.4.4 dplyr_1.0.10 

loaded via a namespace (and not attached):
 [1] sass_0.4.7        utf8_1.2.4        generics_0.1.3    stringi_1.7.12   
 [5] digest_0.6.33     magrittr_2.0.3    evaluate_0.23     grid_4.3.2       
 [9] fastmap_1.1.1     jsonlite_1.8.7    nnet_7.3-19       backports_1.4.1  
[13] DBI_1.1.3         Formula_1.2-5     gridExtra_2.3     purrr_1.0.2      
[17] fansi_1.0.5       scales_1.2.1      jquerylib_0.1.4   cli_3.6.1        
[21] rlang_1.1.2       munsell_0.5.0     base64enc_0.1-3   withr_2.5.0      
[25] cachem_1.0.8      yaml_2.3.7        tools_4.3.2       checkmate_2.1.0  
[29] htmlTable_2.4.2   colorspace_2.1-0  assertthat_0.2.1  vctrs_0.6.4      
[33] R6_2.5.1          rpart_4.1.23      lifecycle_1.0.4   stringr_1.5.0    
[37] htmlwidgets_1.5.4 foreign_0.8-86    cluster_2.1.6     pkgconfig_2.0.3  
[41] pillar_1.9.0      bslib_0.5.1       gtable_0.3.4      data.table_1.14.8
[45] glue_1.6.2        highr_0.10        xfun_0.41         tibble_3.2.1     
[49] tidyselect_1.2.0  rstudioapi_0.14   knitr_1.45        farver_2.1.1     
[53] htmltools_0.5.7   labeling_0.4.2    rmarkdown_2.25    compiler_4.3.2